GnomADFixed

Load packages & data

library(tidyverse)
library(nnet)
library(knitr)
library(tidyr)
library(plotly)
library(ggplot2)
library(dplyr)
library(htmlwidgets)

library(readxl)
RaceFreq_rework <- read_excel("RaceFreq_rework.xlsx")

mybreaks <-c(0.005, 0.046, 0.23,1.0)
myfix <- c(10.0,20.0,60.0,100.0)
mycol <- c('#EF5350', '#EC407A', '#2CD931', '#5E35B1', '#2CD9D1', '#2196F3', '#263238', '#00796B', '#FBC02D')
mybreakscol <-c(0.00, 0.5, 1.0)

plp <- RaceFreq_rework %>%
  mutate(text = paste("Variant: ", mutation_code, "\nFrequency: ", `pop freq. GnomAD`, "\nREVEL: ", `REVEL score`, "\nRace:", Race, sep="")) %>%
  
  # Classic ggplot
  ggplot(aes(x = `AA #`, y = `REVEL score`, size = `Allele Frequency.y`, color = Race, text = text)) +
    geom_point(alpha=0.5) +
    scale_size(range = c(3,80), breaks = mybreaks, name = "") +
    scale_color_manual(values = mycol, name = "") + 
    scale_y_continuous(name="REVEL Score", limits=c(0, 1)) +
    scale_x_continuous(name = "Amino Acid Number", limits = c(0, 2527)) + 
  ggtitle("GnomAD Variants vs REVEL with Frequency") 
# turn ggplot interactive with plotly
ppp <- ggplotly(plp, tooltip="text")

ppp <- ppp %>% layout(legend= list(itemsizing='constant'))
ppp <- ppp %>% layout(legend=list(title=list(text='<b> Race </b>')))


ppp

# save the widget

saveWidget(ppp, file=paste0("GNOMADRaceFreq.html"))